The taxonomic position of Annandale’s rat, Rattus annandalei (Bonhote, 1903), has been uncertain given its mix of Rattus-like and Sundamys-like morphological features. Annandale’s rat and all described species in Sundamys (the lowland S. muelleri, and the montane S. maxi and S. infraluteus) are endemic to Sundaland, a center of diversification and endemism for their tribe, the Rattini. Using mitochondrial genomes and 3 nuclear markers (rag1, rbp3, ghr), we provide the 1st phylogenetic framework for Sundamys. We find that R. annandalei is nested within Sundamys, and that the 4 species likely diverged during the Pleistocene. We move R. annandalei to Sundamys and provide an emended diagnosis for Sundamys. Using geometric morphometric analyses of skulls and mandibles, we identify morphological differences between lowland and highland species of Sundamys that may be associated with adaptations to distinct diets.